Aims Bio-organic fertilizer and different additives are widely applied to suppress soil-borne diseases. However, how different additives alter bulk soil microflora and thereby induce the healthy rhizospheric microflora remains unclear.

Background Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes. Results Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer. Conclusions We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers.

High-quality bio-organic fertilizers (BIOs) cannot be produced without the addition of some proteins. In this study, compound liquid amino acids (CLAA) from animal carcasses were utilized as additives into matured composts to create novel BIOs containing plant growth-promoting rhizobacteria (PGPR). The results showed that adding CLAA and inoculating bacteria meanwhile resulted in failed solid-state fermentation (SSF) due to the higher H+ contents. While after pre-compost for 4 days before PGPR inoculation, treatments of matured chicken or pig manure added with 0.2 ml g-1 of CLAA resulted in a maximum biomass of functional strains. Illumine-MiSeq sequencing and Real-Time PCR results showed that the CLAA addition decreased the bacterial abundance and richness, altered the bacterial community structure and changed the relative abundance of some microbial groups. This study offers a high value-added utilization of waste protein resources for producing economical, high-quality BIO.

No abstract

Application of plant growth-promoting microbes (PGPMs) can contribute to sustainable agricultural ecosystems. From a three-year field experiment, we already found that the addition of Trichoderma bio-organic fertilizer (BF) significantly improved crop growth and yield compared to the application of organic fertilizer (OF). Here, we tracked the responses of soil bacterial and fungal communities to these treatments to find the key soil microbial taxa that contribute to the crop yield enhancement. We also examined if bacterial and fungal suspensions from resulting soils could improve plant growth upon inoculation into sterilized soil. Lastly, we isolated a number of fungal strains related to populations affected by treatments to examine their role in plant growth promotion. Results showed that consecutive application of BF impacted soil fungal communities, and the biological nature of plant growth promotion was confirmed via pot experiments using γ-sterilized versus none-sterilized soils collected from the field. Soil slurry experiments suggested that fungal, but not bacterial communities, played an important role in plant growth promotion, consistent with the results of our field experimental data. Fungal community analysis of both field and slurry experimental soils revealed increases in specific resident Aspergillus spp. Interestingly, Aspergillus tamarii showed no plant growth promotion by itself, but strongly increased the growth promotion activity of the Trichoderma amendment strain upon their co-inoculation. The effectiveness of the fungal amendment appears to stem not only from its own action, but also from synergetic interactions with resident fungal populations activated upon biofertilizer application.